[Bio-linux-dev] Corruption of persistent filesystem on USB-stick

Tim Booth tbooth at ceh.ac.uk
Tue Mar 18 07:02:29 EDT 2014


Hi Tony,

Thanks for the info.  I already have code to repartition the sticks
because that's how the old usb-maker worked.  We switched to using a
loopback file because the partitioning brought its own problems.

I think it should be reasonably easy to combine the versions and make a
usb-maker that can handle either partitioning or loopback.  Given the
4GB size limitation for FAT 32 and that we now have a nice batch of 8GB
sticks I'll probably need to do this anyway, regardless of the
corruption issue.

Cheers,

TIM

On Tue, 2014-03-18 at 10:32 +0000, Tony Travis wrote:
> On 28/02/14 13:51, Tim Booth wrote:
> > Hi Tony,
> >
> > Thanks for the patch.  I'd thought about the 4GB limit in regard to
> > image size but totally forgot about casper-rw.  I'm surprised to see it
> > manifest as filesystem corruption without warning though - I'd expect to
> > see an error during the USB stick creation.
> >
> > Let me know if it fixes the issues and I'll patch the package.
> 
> Hi, Tim.
> 
> Limiting the size of casper-rw to 4095 MiB does NOT fix the problem, but
> creating a separate partition of the disk for casper-rw DOES!
> 
> The corrupted sticks could still be booted read-only if you edit the
> GRUB command-line by pressing F6 at the boot menu and remove the work
> "persistent". The problem might be to do with using FAT32 to store a
> casper-rw container file, but ext3 is more robust if the filesystem is
> not sync'ed properly on shutdown. I had similar problems with the USB
> sticks I created for the NuGO project, but we thought that was due to
> using poor quality USB sticks.
> 
> There has been quite a lot of discussion about this on the Internet, but
> it doesn't BITE unless you make non-trivial use of the casper-rw.
> 
> Attached is my patch for manually partitioned USB-ticks. I'll post
> another patch when I've added some code to re-partition the sticks.
> 
> Bye,
> 
>   Tony.
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> The University of Aberdeen is a charity registered in Scotland, No SC013683.

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
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